Created generate_probesetfreeze_file to create the

"probesetfreeze data matrix" file corresponding with the
muscle dataset Evan was having trouble with

1 files changed, 123 insertions, 0 deletions

diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
new file mode 100644
index 00000000..95515cea
--- /dev/null
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -0,0 +1,123 @@
+#!/usr/bin/python
+
+from __future__ import absolute_import, print_function, division
+
+import sys
+
+sys.path.insert(0, "..")
+
+import os
+import collections
+import csv
+
+import MySQLdb
+
+from base import webqtlConfig
+
+from pprint import pformat as pf
+
+
+def get_cursor():
+    con = MySQLdb.Connect(db=webqtlConfig.DB_UPDNAME,
+                          host=webqtlConfig.MYSQL_UPDSERVER,
+                          user=webqtlConfig.DB_UPDUSER,
+                          passwd=webqtlConfig.DB_UPDPASSWD)
+    cursor = con.cursor()
+    return cursor
+
+def show_progress(process, counter):
+    if counter % 1000 == 0:
+        print("{}: {}".format(process, counter))
+
+def get_strains(cursor):
+    cursor.execute("""select Strain.Name
+                      from Strain, StrainXRef, InbredSet
+                      where Strain.Id = StrainXRef.StrainId and
+                            StrainXRef.InbredSetId = InbredSet.Id
+                            and InbredSet.Name=%s;
+                """, "BXD")
+    
+    strains = [strain[0] for strain in cursor.fetchall()]
+    print("strains:", pf(strains))
+    for strain in strains:
+        print(" -", strain)
+    
+    return strains
+
+def get_probeset_vals(cursor, dataset_name):
+    cursor.execute(""" select ProbeSet.Id, ProbeSet.Name
+                from ProbeSetXRef,
+                     ProbeSetFreeze,
+                     ProbeSet
+                where ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and
+                      ProbeSetFreeze.Name = %s and
+                      ProbeSetXRef.ProbeSetId = ProbeSet.Id;
+            """, dataset_name)
+    
+    probesets = cursor.fetchall()
+    
+    print("Fetched probesets")
+    
+    probeset_vals = collections.OrderedDict()
+    
+    for counter, probeset in enumerate(probesets):
+        cursor.execute(""" select Strain.Name, ProbeSetData.value
+                       from ProbeSetData, ProbeSetXRef, ProbeSetFreeze, Strain
+                       where ProbeSetData.Id = ProbeSetXRef.DataId
+                       and ProbeSetData.StrainId = Strain.Id
+                       and ProbeSetXRef.ProbeSetId = %s
+                       and ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId
+                       and ProbeSetFreeze.Name = %s;
+                """, (probeset[0], dataset_name))
+        val_dic = collections.OrderedDict()
+        vals = cursor.fetchall()
+        for val in vals:
+            val_dic[val[0]] = val[1]
+        
+        probeset_vals[probeset[1]] = val_dic
+        show_progress("Querying DB", counter)
+        
+    return probeset_vals
+
+def trim_strains(strains, probeset_vals):
+    trimmed_strains = []
+    #print("probeset_vals is:", pf(probeset_vals))
+    first_probeset = list(probeset_vals.itervalues())[0]
+    for strain in strains:
+        print("\n**** strain is:", pf(strain))
+        print("\n**** first_probeset is:", pf(first_probeset))
+        if strain in first_probeset:
+            trimmed_strains.append(strain)
+    print("trimmed_strains:", pf(trimmed_strains))
+    return trimmed_strains
+
+def write_data_matrix_file(strains, probeset_vals, filename):
+    with open(filename, "wb") as fh:
+        csv_writer = csv.writer(fh, delimiter=",", quoting=csv.QUOTE_ALL)
+        #print("strains is:", pf(strains))
+        csv_writer.writerow(['ID'] + strains)
+        for counter, probeset in enumerate(probeset_vals):
+            row_data = [probeset]
+            for strain in strains:
+                #print("probeset is: ", pf(probeset_vals[probeset]))
+                row_data.append(probeset_vals[probeset][strain])
+            #print("row_data is: ", pf(row_data))
+            csv_writer.writerow(row_data)
+            show_progress("Writing", counter)
+
+def main():
+    filename = os.path.expanduser("~/gene/wqflask/maintenance/" +
+                "ProbeSetFreezeId_379_FullName_EPFL_LISP_BXD_CD_Muscle_Affy_Mouse_Gene_1.0_ST_" + 
+                "(Dec11)_RMA_**.txt")
+    dataset_name = "EPFLMouseMuscleCDRMA1211"
+
+    cursor = get_cursor()
+    strains = get_strains(cursor)
+    print("Getting probset_vals")
+    probeset_vals = get_probeset_vals(cursor, dataset_name)
+    print("Finished getting probeset_vals")
+    trimmed_strains = trim_strains(strains, probeset_vals)
+    write_data_matrix_file(trimmed_strains, probeset_vals, filename)
+
+if __name__ == '__main__':
+    main()